► Of the approximate 300 currently recognised bat species known from the Afrotropics, very few have been studied in sufficient detail to a) provide accurate species…
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▼ Of the approximate 300 currently recognised bat species known from the Afrotropics, very few
have been studied in sufficient detail to a) provide accurate species and distributional limits for
extant taxa, b) identify possible cryptic species, and c) ascertain the closest sister lineage of
numerous taxonomic groups. For those species where DNA-based phylogenies are available,
the use of additional taxonomic markers and methods has provided further insights into the
evolutionary history of certain extant chiropteran groups. This work comprises a series of
systematic studies of African and Malagasy Chiroptera aimed at investigating sequence-based
evolutionary hypotheses of higher and lower level taxa using comparative molecular cytogenetic
and morphometric techniques.
Efforts were directed at resolving taxonomic inconsistencies of chiropteran taxa from the African
subregion and/or Madagascar, for which there is a general paucity of comprehensive and/or
resolved phylogenies. Taxa belonging to the families Pteropodidae, Hipposideridae,
Myzopodidae, and Molossidae were chosen for study because molecular-based have failed to
provide consensus regarding evolutionary relationships amongst the above-mentioned
taxonomic groups, or are in stark contrast to phylogenies based on morphological data. In
addition, molecular cytogenetics and geometric morphometric approaches were used because
they have had been applied in few evolutionary studies of Afrotropical bats.
With the exception of a few karyotypic descriptions, scant data are available that details the
chromosomal diversity and karyotypic evolution of bats from Madagascar in relation to their
conspecifics or congenerics on other continents. To understand better the mechanisms that
may have structured the karyotypes of extant Malagasy Chiroptera and the utility of
chromosomal characters in retracing their evolutionary history, eight species from seven
families were analysed using G- and C-banding and chromosome painting. Robertsonian (Rb)
fusions and fissions were the dominant mode of genome restructuring amongst taxa and, for the
most part, proved useful characters for investigations of phylogenomic relationships amongst
families and genera.
Chromosomal data generated from painting studies employing Myotis myotis (MMY)
chromosomal probes, produced phylogenetically important characters that supported two
conflicting hypotheses regarding the evolutionary affinities of the Myzopodidae, a family of bats
endemic to Madagascar. The Rb fusion MMY 9+11 detected in Myzopodidae, also common to
Phyllostomidae, could suggest a close association of Myzopoda aurita with the superfamily
Noctilionoidea. However, the Rb fusion MMY 3+4 that is also present in vesper bats, suggests
closer evolutionary ties between M. aurita and the Vespertilionoidea. A sex-autosome
translocation, a cytogenetic character previously confined to phyllostomid and vespertilionid
bats, was also detected in M. aurita casting further uncertainties on the evolutionary origins of
this deep-branching species. This study…
Advisors/Committee Members: Lamb, Jennifer M (advisor), Taylor, Peter John (advisor), Schoeman, Corrie M (advisor), Goodman, Steven M (advisor).

► Anabolic steroid abuse remains the most potent and frequent form of doping in elite sports, originally utilising synthetic potent anabolic steroids. However, advances in highly…
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▼ Anabolic steroid abuse remains the most potent and frequent form of doping in elite sports, originally utilising synthetic potent anabolic steroids. However, advances in highly sensitive mass spectrometry-based urine drug screens for synthetic anabolic steroids has led to exploits in the illicit use of the natural anabolic steroid testosterone, which is difficult to distinguish between the endogenous form of testosterone. Glucuronidation, performed by UDP glucuronosyltransferases (UGTs), is a key process for inactivation of anabolic steroids before excretion. The key enzyme involved in testosterone glucuronidation is UGT2B17, in contrast to epitestosterone which is mainly glucuronidated by UGT2B7. Changes in the regulation of these enzymes could alter excreted concentrations of these steroids and affect urinalysis, performed to determine testosterone doping in sport. Literature reports reveal alterations to testosterone glucuronidation through inhibition and pharmacogentic variations of UGT2B17, along with the interaction of epitestosterone on testosterone glucuronidation. This study aims to investigate the role of compounds commonly found in dietary substances such as teas and red wine samples, along with pharmaceuticals on UGT mediated testosterone and epitestosterone glucuronidation. The interaction of epitestosterone and stanozolol on testosterone glucuronidation was also investigated. HPLC and LC-MS/MS analysis were used to monitor levels of testosterone and epitestosterone glucuronidation following UGT supersome and microsome based assays in vitro. A rat model was used to investigate the role of diclofenac and stanozolol on excreted testosterone and epitestosterone. An LC-MS/MS method capable of measuring 0.125 ng/mL testosterone and 0.250 ng/mL epitestosterone (deconjugated) in rat blood and urine was optimised and validated. Dietary green and white teas along with red wine inhibit UGT2B17 testosterone glucuronidation and UGT2B7 epitestosterone glucuronidation. The inhibitory activities of constituent catechin and phenolic compounds against these enzymes have been determined. In an in vivo study, stanozolol reduced the long term excretion levels of testosterone, coupled to increased epitestosterone excretion and reduced T/E ratios. On the other hand diclofenac did not appear to alter excreted testosterone and epitestosterone levels, apart from having a short term effect on T/E levels. This study demonstrates the role of dietary, pharmaceutical and steroid interactions on UGT testosterone and epitestosterone glucuronidation, along with an evaluation of the consequences linked with enhanced anabolic steroid levels and anti-doping regulation.

► Tachykinins are signalling peptides released by the processing of preprotachykinin precursors, which are subject to post-translational modifications including amidation. Tachykinins act on the three tachykinin…
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▼ Tachykinins are signalling peptides released by the processing of preprotachykinin precursors, which are subject to post-translational modifications including amidation. Tachykinins act on the three tachykinin receptors NKl, NK2 and NK3. Differential processing of the preprotachykinin precursors can lead to the formation of a diverse range of tachykinins (including extended forms). Our previous findings have shown increased proteolytic cleavage of the human TAC3 and TAC4 preprotachykinin precursors by the placenta in pathological conditions such as pre-eclampsia comparable to that found in the brain. This study has developed an experimental strategy for the capture and detection of tachykinins combining peptide extraction, enrichment by immunoaffinity purification, RP-HPLC separation and MALDI-TOF. The combined application of these methods in rat brain identified mHK-l as an amidated decapeptide and also captured and detected SP. The detection of a modified form of mHK-l in the brain matching the mass of an additional acetyl group (+42 a.m.u.) indicates the existence of a neuropeptide-specifie post-translational modification. The biological role of acetylation is to provide greater stability for the peptide and affinity of binding for its receptor. The methodology described in this research could be applied for the capture of tachykinins expressed in normal, pre-eclamptic and IUGR placentae, in order to investigate the changes that occur in precursor processing during disease states such as pre-eclampsia and to identify post-translational modifications. A parallel in silico analysis of the publicly accessible NCBI and Ensembl databases was conducted to identify tachykinin precursors. Multiple sequence alignment of retrieved preprotachykinin sequences was conducted and the phylogenetic relationship between the identified species investigated. Collectively, the results expand the number of known or predicted tachykinins and tachykinin gene-related peptides. Moreover, they separate the preprotachykinin precursors into three distinct groups. The analysis also sheds lights on the evolution of the tachykinin precursor cleavage sites (e.g. the N-terminal monobasic cleavage site of human EKA/B). Overall, this study has developed technologies for identifying tachykinin precursor post-translation modifications that may serve as a tool for determining different peptide physiologies between neuronal and peripheral tissues and different disease states.

Deliconstantinos, G. (2013). Method development for identification of tachykinins and their post-translational modifications and discovery with in silco analysis of bio-informatic databases. (Doctoral Dissertation). Kingston University. Retrieved from http://eprints.kingston.ac.uk/26560/ ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.587387

Chicago Manual of Style (16th Edition):

Deliconstantinos, Gina. “Method development for identification of tachykinins and their post-translational modifications and discovery with in silco analysis of bio-informatic databases.” 2013. Doctoral Dissertation, Kingston University. Accessed January 21, 2019.
http://eprints.kingston.ac.uk/26560/ ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.587387.

MLA Handbook (7th Edition):

Deliconstantinos, Gina. “Method development for identification of tachykinins and their post-translational modifications and discovery with in silco analysis of bio-informatic databases.” 2013. Web. 21 Jan 2019.

Deliconstantinos G. Method development for identification of tachykinins and their post-translational modifications and discovery with in silco analysis of bio-informatic databases. [Doctoral Dissertation]. Kingston University; 2013. Available from: http://eprints.kingston.ac.uk/26560/ ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.587387

▼ The present study focused on protein kinase C (pKC), extracellular signal-regulated kinase (ERK) and p38 mitogen-activated protein kinase (p38 MAPK) signalling in the human parasite Schistosoma mansoni, with a focus on life-stages which are human infective and dependent (cercariae, schistosomules and adult worms). Western blotting with anti-phospho antibodies, detected two phosphorylated PKC 081 kDa and ~ 116 kDa) and two phosphorylated ERK (~43 kDa and ~48 kDa) isotypes predicted in the S. mansoni genome in addition to the previously identified ~78 kDa PKC and ~42 kDa p38 MAPK (Ludtmann et al., 2009; Ressurreíçâo et al., 20lla,b). Additionally, an unusually large ~132 kDa PKC-like protein was detected that is not predicted in the genome. These proteins possessed enzymatic activities, responded to conventional activators and inhtbitors, and their activation profile was dissimilar between life-stages suggesting isotype distinct roles in each developmental stage. In vitro challenge with praziquantel stimulated activity of specific PKC and ERK isotypes, showing a putative involvement in the mode of action of this anthelmintic drug. In situ localization revealed the activated kinases associated with several regions including tegument, sensory, neuromuscular and reproductive structures; additionally, phosphorylated ERK was associated with the excretory system. PKC, ERK and p38 MAPK function was assessed through pharmacological and environmental assays. PKC and ERK were found to playa role in pairing, motility, ventral sucker attachment and egg output of adult worms and motility of schistosomules. Maintenance of unpaired adult worms in different sex ratio environments resulted in changes in PKC, ERK and p38 MAPK activity (both in male and females) showing importance in transduction of chemotatic and/or thigmotatic stimuli. Light and temperature changes affected kinase activity in cercariae mainly at the cercariae sensory papillae and parasite surface. Moreover, combined linoleic acid (LA) and CFDA-SE based assays developed for induction and monitoring of cercarial gland release showed that PKC, ERK and p38 MAPK are involved in mechanisms that underpin cercariae host detection/penetration and that pharmacological inhibition of these enzymes partially blocked LA induced release, while the PKC activator accelerated it. In schistosomules, epidermal growth factor and insulin stimulated ERK and PKC activity whereas insulin-like growth factor I and mouse red blood cells up¬regulated PKC activity only suggesting association with parasite nutrition and host-parasite communication. Internalization of fluorescently labelled transferrin via the schistosomule tegument was delayed with PKC inhibitors suggesting a role in transferrin uptake. Taken together, these data contribute significantly to our understanding of cell signalling in schistosomes and how such signalling regulates parasite function, and should open up new avenues of investigation for development of anti-schistosome drugs.

► The age and origins of large earth mounds (locally termed "heuweltjies") is under debate, with ages being proposed for between 4500 and 30 000 years…
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▼ The age and origins of large earth mounds (locally termed "heuweltjies") is under debate, with ages being proposed for between 4500 and 30 000 years old, and hypotheses including zoogenic and geological origins of the mounds. The widely accepted hypothesis for the origins of the heuweltjies found in the South Western Cape of South Africa is that mounds are ancient termitaria, belonging to the southern harvester termite Microhodotermes viator. Our idea was to use rocks and stone layer profiles to determine approximate ages of the heuweltjies as well as to gather evidence to either support or refute the termite hypothesis. We excavated ten mounds in Clanwilliam, South Africa, to gather stone and rock profiles throughout the mounds, as well as digging a trench through a heuweltjie with bedrock as its matrix in order to determine the extent of the bedrock into the mound. No stone layers as such were found. What we did find was that the mounds are a whole order of magnitude greater in volume than large termite mounds made by the northern harvester termite Macrotermes in tropical regions, and many of the mounds contain large rocks both throughout the mound as well as on the surface. The trench cut through the mound on bedrock revealed the bedrock extending all the way to the centre of the mound, on the same level as the surface of the surrounding matrix. This evidence can be used to refute the termite hypothesis for the heuweltjies of Clanwilliam as it is virtually impossible for termites to move rocks up to 25 kg to the top of a mound, and mining soil from beneath a mound with bedrock at its base is an impossibility.
Advisors/Committee Members: Midgley, Jeremy J, Cramer, Michael D.

Innes, S. (2010). Contesting the termite hypothesis for the origins of heuweltjies in Clanwilliam, South Africa. (Thesis). University of Cape Town. Retrieved from http://hdl.handle.net/11427/26386

Note: this citation may be lacking information needed for this citation format:Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16th Edition):

Innes, Sheona. “Contesting the termite hypothesis for the origins of heuweltjies in Clanwilliam, South Africa.” 2010. Thesis, University of Cape Town. Accessed January 21, 2019.
http://hdl.handle.net/11427/26386.

Note: this citation may be lacking information needed for this citation format:Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7th Edition):

Innes, Sheona. “Contesting the termite hypothesis for the origins of heuweltjies in Clanwilliam, South Africa.” 2010. Web. 21 Jan 2019.

Vancouver:

Innes S. Contesting the termite hypothesis for the origins of heuweltjies in Clanwilliam, South Africa. [Internet] [Thesis]. University of Cape Town; 2010. [cited 2019 Jan 21].
Available from: http://hdl.handle.net/11427/26386.

Note: this citation may be lacking information needed for this citation format:Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Innes S. Contesting the termite hypothesis for the origins of heuweltjies in Clanwilliam, South Africa. [Thesis]. University of Cape Town; 2010. Available from: http://hdl.handle.net/11427/26386

Note: this citation may be lacking information needed for this citation format:Not specified: Masters Thesis or Doctoral Dissertation

University of Cape Town

6.
McGrath, Alice.
Modelling the effects of spatio-temporal spawning variability on the transport and retention success of sardine (Sardinops sagax) eggs and larvae around South Africa.

► The transport and retention of sardine (Sardinops sagax) eggs on the west and south coasts of South Africa were investigated using a Lagrangrian, particle tracking,…
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▼ The transport and retention of sardine (Sardinops sagax) eggs on the west and south coasts of South Africa were investigated using a Lagrangrian, particle tracking, individual-based model (IBM), coupled with two 3-D hydrodynamic Regional Ocean Modeling System (ROMS) model configurations of different generations. The same IBM is coupled with PLUME, an older ROMS model configuration used in a previous sardine IBM for the southern Benguela, as well as BENGSAFE, a more recent, better resolved ROMS model configuration. Results from the two runs were compared to see if and how the underlying ocean model affects modelled retention and transport. An updated IBM, extended spatially and temporally to better represent sardine spawning and recruitment, was then coupled with the BENGSAFE model configuration, and assessed. The effects of spawning area, and month, year and depth of particle release, were investigated for each coupled 3D-IBM simulation using linear models. The portion of particles transported from the south coast to the west coast was a focus throughout, as this is of great importance to the management of the sardine fishery. In all simulations, three main systems were identified depending on where particles were released and recruited. Two of these systems were retention-based: particles released on the west coast and retained in the west coast recruitment area (WC-WC), and particles released on the south coast and retained in the south coast recruitment area (SC-SC). The other system is transport-based and represents particles released on the south coast and transported by ocean dynamics to recruit in the west coast recruitment area. Results were similar for the west coast when either hydro- dynamic model configuration was used; depth of release proved to be important in this system with its effect varying depending where on the west coast particles were released. Differences occurred on the south coast, with more transport to the west coast and more offshore loss in the higher resolved BENGSAFE IBM than the PLUME IBM. The difference was attributed to the positioning of the PLUME model's boundary in close proximity to the Agulhas Current, and the conditions at this boundary not properly resolving the current. The initial BENGSAFE IBM was spatially restricted to match the PLUME IBM, and therefore south coast spawning and recruitment was not fully represented. Therefore, the BENGSAFE IBM was spatially extended on the south coast and run for a longer time period. Similar results were obtained in the extended BENGSAFE IBM and the initial BENGSAFE IBM. However south coast retention increased and the average percentage of particles transported to the west coast decreased slightly. Spawning area proved to be an important determinant of retention and transport success in all recruitment systems, and the further east a particle was spawned the less likely it was to be transported to the west coast, and the more likely it was to be retained on the south coast. Transport to the west coast was most successful in late winter;…
Advisors/Committee Members: Moloney, Coleen L, Van der Lingen, Carl D, Hermes, Juliet C, Roy, Claude.

McGrath, A. (2018). Modelling the effects of spatio-temporal spawning variability on the transport and retention success of sardine (Sardinops sagax) eggs and larvae around South Africa. (Masters Thesis). University of Cape Town. Retrieved from http://hdl.handle.net/11427/27995

Chicago Manual of Style (16th Edition):

McGrath, Alice. “Modelling the effects of spatio-temporal spawning variability on the transport and retention success of sardine (Sardinops sagax) eggs and larvae around South Africa.” 2018. Masters Thesis, University of Cape Town. Accessed January 21, 2019.
http://hdl.handle.net/11427/27995.

MLA Handbook (7th Edition):

McGrath, Alice. “Modelling the effects of spatio-temporal spawning variability on the transport and retention success of sardine (Sardinops sagax) eggs and larvae around South Africa.” 2018. Web. 21 Jan 2019.

Vancouver:

McGrath A. Modelling the effects of spatio-temporal spawning variability on the transport and retention success of sardine (Sardinops sagax) eggs and larvae around South Africa. [Internet] [Masters thesis]. University of Cape Town; 2018. [cited 2019 Jan 21].
Available from: http://hdl.handle.net/11427/27995.

Council of Science Editors:

McGrath A. Modelling the effects of spatio-temporal spawning variability on the transport and retention success of sardine (Sardinops sagax) eggs and larvae around South Africa. [Masters Thesis]. University of Cape Town; 2018. Available from: http://hdl.handle.net/11427/27995

University of Cape Town

7.
Rogers, Annabelle J.
Anthropogenic modification of the natural fire landscape and its consequences for vegetation patterns on the Cape Peninsula.

► Understanding the spatial probability of fire and how urban development may alter natural patterns is particularly important in areas where alternate ecosystem states occur at…
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▼ Understanding the spatial probability of fire and how urban development may alter natural patterns is particularly important in areas where alternate ecosystem states occur at fine spatial scales. The Cape Peninsula, South Africa, is a one such region where fire-sensitive forest patches occur interspersed in a sea of fire-dependent fynbos. Fire is believed to be an important determinate of forest distribution, with absence or occurrence of fires potentially allowing patch contraction and expansion. In this thesis I use a series of computer models to determine the extent to which anthropogenic development and land transformation have altered the spatial variation in fire likelihood, or the 'burn probability', and its consequence for the distribution of forest on the Cape Peninsula. The two multi-model, fire behaviour simulation systems I use are FlamMap and FARSITE. FARSITE is a deterministic simulation package used globally for discrete event simulation. In an effort to assess the viability of using the FARSITE model for fire prediction in fynbos and the determinants of model accuracy, I predicted fire area for a historical fire on the Cape Peninsula using a variety of fuel models and wind conditions. Following this validation, FlamMap was used to simulate the burn probability of the Cape Peninsula under natural conditions – no urban development present – and transformed conditions – where urban areas mapped as non-burnable fuel models. I then determined changes in forest distribution documented over the last 50 years relative to changes in burn probability as a result of urbanisation. My results show that an increase in urbanisation on the Cape Flats has produced a significant urban shadow effect due to the interruption of natural fire catchments. This urban shadow effect has resulted in an overall increase in area of fire refuges on the Peninsula and expansion of forest, particularly on the more mesic eastern slopes at Kirstenbosch and Newlands. The results strongly support that urban-mediated changes to fire patterns are drivers of forest expansion in this region, and adds further evidence to support the significance of fire in determining biome boundaries in the fynbos.
Advisors/Committee Members: February, Edmund C, Moncrieff, Glenn R, Slingsby, Jasper A.

Rogers, A. J. (2017). Anthropogenic modification of the natural fire landscape and its consequences for vegetation patterns on the Cape Peninsula. (Masters Thesis). University of Cape Town. Retrieved from http://hdl.handle.net/11427/25511

Chicago Manual of Style (16th Edition):

Rogers, Annabelle J. “Anthropogenic modification of the natural fire landscape and its consequences for vegetation patterns on the Cape Peninsula.” 2017. Masters Thesis, University of Cape Town. Accessed January 21, 2019.
http://hdl.handle.net/11427/25511.

Rogers AJ. Anthropogenic modification of the natural fire landscape and its consequences for vegetation patterns on the Cape Peninsula. [Masters Thesis]. University of Cape Town; 2017. Available from: http://hdl.handle.net/11427/25511

► Despite the importance of disease as a wildlife management challenge, baseline research on the epidemiology of pathogens occurring in wildlife populations within both rural and…
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▼ Despite the importance of disease as a wildlife management challenge, baseline research on the epidemiology of pathogens occurring in wildlife populations within both rural and urban landscapes has received little attention to date. The aim of this study was to improve our understanding of wildlife health in human-modified landscapes in South Africa, by providing comparisons of body condition, host-attached tick diversity and tick-borne pathogen (TBP) epidemiology of two common mesocarnivore species, the black-backed jackal (Canis mesomelas) and caracal (Caracal caracal). Jackals (n=46) and caracals (n=27) were sampled from small livestock farmlands in the Central Karoo region, in addition to caracals from farmlands in Namaqualand (n=14), and the urban matrix of the Cape Peninsula (n=16). Body condition was evaluated using both ratio (Body Mass Index) and residual (Ordinary Least Squares) methods, and morphometry was compared with historical datasets for each species. There was no apparent effect of sex, age class or location on body condition of jackals or caracals. Host-attached tick diversity was highest in urban caracals compared with the two other caracal populations, possibly indicating that they are exposed to a greater diversity of potential tick vectors. Molecular methods (mPCR/RLB; conventional PCR screening and phylogenetic analysis) used to screen for selected pathogens of veterinary and/or zoonotic concern, including Ehrlichia, Anaplasma, Babesia and Theileria species, revealed that Central Karoo jackals exhibited a lower prevalence of TBPs, compared with sympatric caracals. Hepatozoon canis, a ubiquitous pathogen of domestic and wild canids globally, was observed in 46.5% of jackals. Theileria ovis, a piroplasm of small livestock, was found in 4.7% of jackals. Jackals and caracals appear to be distinct in their TBP epidemiological roles, despite sharing similar tick communities. Pathogens found in caracals include Hepatozoon felis, Babesia felis, Babesia leo and a potentially undescribed Babesia species, genetically similar to B. venatorum, an emerging zoonosis. An Anaplasma species previously described in South African domestic dogs was also found in the urban caracals. All caracals were infected with at least one TBP. Together, these findings suggest that land use does not significantly influence the body condition of these adaptable predators, but that there is a health cost associated with living in the urban space. Cape Peninsula caracals show substantially higher rates of TBP co-infection (81% versus 14.8% and 0% in farmlands) and greater pathogen diversity compared to farmland caracals. The findings of this study include numerous examples of previously undescribed genetic diversity of tick-borne pathogens infecting South African mesocarnivores living in transformed landscapes. This work adds to our understanding of wildlife health within the 'One Health' framework and represents the first detailed examination of TBPs in jackals on farmlands and is also the first work that focuses specifically on…
Advisors/Committee Members: Bishop, Jacqueline M, O'Riain, M Justin.

► Neuropeptides of the adipokinetic hormone/red pigment concentrating hormone (AKH/RPCH) family are well known as regulators for many physiological processes in insects, notably energy metabolism, and…
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▼ Neuropeptides of the adipokinetic hormone/red pigment concentrating hormone (AKH/RPCH) family are well known as regulators for many physiological processes in insects, notably energy metabolism, and a possible role in myostimulation. The Indian stick insect Carausius morosus contains two members of this family, hypertrehalosaemic hormone I and II (Carmo-HrTH-I and -II). Both these are decapeptides and they differ only at position 8, where the tryptophan of Carmo-HrTH-I is C‐mannosylated. It is known that Carmo-HrTHs increase the carbohydrate (trehalose) concentration in the haemolymph via a G protein-coupled receptor. The current study seeks to identify which part of the HrTH amino acid sequence is necessary to interact with the receptor on the fat body of C. morosus to trigger a response (hypertrehalosaemia) eventually leading to the release of carbohydrates into the haemolymph. In addition, the role of Carmo-HrTHs in stimulating the heart rate through myostimulation was also investigated. Two biological assays were used to assess the potencies of various analogues, in comparison to that of the native peptides: (1) the carbohydrate-mobilizing assay assessed the increase in levels of carbohydrates; and (2) the semi-exposed heart assay assessed the increase in heart rates. The current study confirmed that both Carmo-HrTH-I and -II are capable of increasing the haemolymph carbohydrates in ligated stick insects. The results of the current study revealed, for the first time, that these peptides also similarly stimulate the heart rate of the stick insect. Thus, Carmo-HrTH-II was used as a lead peptide in the current study on which various naturally-occurring AKH peptides and systematically altered analogues were based. The selected naturally-occurring AKH peptides had a single or double amino acids replacement in comparison to Carmo-HrTH-II and some were octapeptides. Each systematically altered analogue of the native Carausius HrTH II had a single amino acid replaced with alanine. Additionally, two analogues that lacked the N-terminal pyroglutamate residue or had a free threonine acid at the C-terminus instead of an amide were also tested. The results showed that the N- or C- terminal modified analogues have no hypertrehalosaemic activity in C. morosus and are also incapable of increasing the heart rate of this insect as high as Carmo-HrTH-II. This suggests that the blocked termini are important features, for both peptide protection and receptor binding. The structural requirements of C. morosus receptor(s) for Carmo-HrTHs appear to be very specific. The receptor(s) do not accept octapeptides and only four out of the fourteen decapeptides elicited at least 46% of the biological activity as compared to the native peptide and the rest (ten) were not active. This implies that the HrTHs receptor (s) for C. morosus do not tolerate the replacement of most single amino acids. In the heart assay, known cardio-stimulatory peptides were applied to the semi-exposed heart of C. morosus to establish the potential extent of…
Advisors/Committee Members: Marco, Heather G, Gäde, Gerd.

► Breast cancer is the second most represented cancer type worldwide and will affect 1 in 8 women in the UK. Overall patient survival can reach…
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▼ Breast cancer is the second most represented cancer type worldwide and will affect 1 in 8 women in the UK. Overall patient survival can reach 90% when the disease is diagnosed early but rapidly drops as the tumour progresses and metastasises. The steps required for tumour formation are known but numerous factors are involved and the specific mechanisms controlling this phenomenon are still poorly understood. WSB-1 is a hypoxia-responsive E3 ubiquitin ligase which was found to be upregulated in metastatic tissues, compared to normal or non invasive tissues. In addition, studies demonstrated that WSB-1 was involved in pancreatic cancer, neuroblastoma, and osteosarcoma progression. However, its role in breast cancer has not been particularly studied. The objective of this thesis is to study the role of WSB-1 in breast cancer. Initially, level of WSB1 in patients' tumour cDNA samples was evaluated according to known clinical and biological variables. Impact of high WSB1 levels on patients' distant metastasis-free survival, relapse-free survival and overall survival was also investigated. Then, the effect of WSB-1 knockdown on protein levels of epithelial to mesenchymal transition markers, as well as several matrix metalloproteinases (MMP) transcript and protein levels, and activity was examined. Consequence of these modifications on cell motility (migration, invasion) was studied, using single cells, cellular monolayers and spheroids. Finally, affinity purification followed by mass spectrometry was used to identify novel WSB-1 partners. Overall, in MDA-MB-231 cells, WSB-1 appeared to drive metastasis formation by upregulating MMPs expression and activity, promoting EMT and inducing invasiveness. WSB-1 had a more conflicting effect in MCF7 cells. In fact, WSB-1 effect appeared to be depending on the ER- and ER+ status. Together, these results validated WSB-1 as an important player in breast cancer development, particularly in metastasis formation.

Poujade, F. (2016). Investigating the role of WSB-1 in breast cancer. (Doctoral Dissertation). University of Hull. Retrieved from http://hydra.hull.ac.uk/resources/hull:15421 ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.721531

Chicago Manual of Style (16th Edition):

Poujade, Flore-Anne. “Investigating the role of WSB-1 in breast cancer.” 2016. Doctoral Dissertation, University of Hull. Accessed January 21, 2019.
http://hydra.hull.ac.uk/resources/hull:15421 ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.721531.

Poujade F. Investigating the role of WSB-1 in breast cancer. [Doctoral Dissertation]. University of Hull; 2016. Available from: http://hydra.hull.ac.uk/resources/hull:15421 ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.721531

Synaptic plasticity, the ability of synapses to undergo changes in their strength, forms the basis for memory formation. Transcription and translation is required to establish…
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▼

Synaptic plasticity, the ability of synapses to
undergo changes in their strength, forms the basis for memory
formation. Transcription and translation is required to establish
such long term changes at synapses. In this thesis, I present
results from my studies about how these complex processes are
newlineorchestrated to produce diverse cellular responses. We have
developed a biochemical model of plasticity-triggered protein
synthesis. This model was constrained by reproducing experimental
data. We have shown that protein synthesis is high in a narrow
range of calcium levels and is gated by BDNF. We found that these
properties prevent newlinerunaway activation of the pathway.
Despite several positive feedback loops in the model, we have also
shown that bistability is unlikely to arise. It is known that
different kinds of inputs lead to synthesis of different subsets of
mRNA and proteins but the mechanism is unclear. We built a model of
key regulatory pathways that control neuronal mRNA synthesis, based
on published experimental data. We found that this network
newlinedecodes a wide range of temporal stimuli implicated in
synaptic plasticity, and generates distinct combinations of mRNA
transcripts in response. To explore how this differentially
synthesized mRNA is delivered from the nucleus, our model can be
incorporated with rate of mRNA transport. We designed an experiment
to measure the speed and distance of its transport. We conducted
preliminary experiments where we observed BDNF and PKM-zeta mRNA
after inducing plasticity in a hippocampal slice, by using
fluorescent in situ hybridization (FISH). newlineOur simulation
study coupled with experiments provides a framework to study the
regulation of differential protein synthesis during transport and
at the synapse.

► The consequences of predation have become a central focus of marine ecological research. Numerous studies have emphasized the importance of apex predators in structuring assemblages…
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▼ The consequences of predation have become a central focus of marine ecological research. Numerous studies have emphasized the importance of apex predators in structuring assemblages at various organisational levels and in determining how ecosystems function. However, less appreciated currently is the fact that predators display multiple foraging behaviours, thereby allowing them to overcome problems associated with unpredictability of food resources in space and time. The primary goal of this dissertation is to contribute to growing understanding of the ecological causes and consequences of foraging plasticity displayed by Greater Flamingo Phoenicopterus ruber roseus in intertidal sandflat ecosystems in Langebaan Lagoon, South Africa. P. roseus feeds by either (1) creating pits, which involves flamingos stirring up deep sediments with their feet or (2) creating channels, in which their inverted bills are swept from side-to-side on the sediment surface. The first objective of the study was to quantify the ecological drivers of decisions made by flamingos to feed, and to implement either pit- or channel-foraging strategies. The latter was achieved through RandomForest modelling techniques that identified the prominent ecological drivers from a suite of biotic and abiotic variables. Results indicate that biotic variables, i.e. those associated with flamingo prey assemblages, were key in driving choices made by flamingos to forage and to implement either pit- or channel-foraging strategies. The second aim of this dissertation was to quantify the repercussions of the two different foraging behaviours on benthic assemblages. Comparisons of benthic assemblages in flamingo foraging structures (pits and channels) with adjacent non-foraged sediments (controls) indicated differential effects of both flamingo foraging methods on benthic communities, with channel-foraging eliciting a greater negative impact compared to pit-foraging, for which impacts were negligible. Abundance of macrofauna and surface-dwelling taxa such as micro-algae and the amphipod Urothoe grimaldii were all negatively impacted by channel-foraging. Sizes of channels constructed by flamingos were inversely related to their impacts, with impacts on macrofaunal abundance being greater in smaller channels. Overall, this study has shed light on the differential effects of foraging plasticity on prey assemblages and its importance in enhancing spatio-temporal heterogeneity in intertidal sandflats. The study also emphasizes the need to incorporate foraging plasticity into current thinking and conceptual models of predation in marine soft sediments, in order to appreciate the full spectrum of predation effects on assemblages.
Advisors/Committee Members: Pillay, Deena, Varughese, Melvin.

► Aloe species are common in Kenya and have many health benefits which include promotion of wound healing, antifungal activity, hypoglycemic or anti-diabetic effects, antiinflammatory and…
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▼ Aloe species are common in Kenya and have many health benefits which include promotion of wound healing, antifungal activity, hypoglycemic or anti-diabetic effects, antiinflammatory
and anticancer properties. However, little has been done to study the genetic variability of Aloe species in Kenya. Fusarium oxysporum and Pythium ultimum are economically important plant pathogens with a wide host range causing several diseases including root rots and damping off. The objectives of this study were to genetically characterize Aloe species found in Kenya and assess the efficacy of their extracts on Fusarium oxysporum and Pythium ultimum. Thirty one morphologically diverse Aloe species were sampled from ex-situ and in-situ collections. Morphological characterization was done using leaf color, presence or absence of variegation and color of spines. DNA extraction was carried out using cetyl trimethyl ammonium bromide (CTAB) method. Sequence related amplified polymorphism (SRAP) markers were used to determine genetic diversity of the Aloe species Forty eight primer pairs were screened to select those that had the highest number of polymorphisms. Eight primer pairs, which were polymorphic, were selected to genotype the Aloe species. Crude extracts of the leafs were made by extracting with dichloromethane: methanol in the ratio of 1:1 and made into concentrations of 100mg/100|il, 50mg/100pl, 25mg/100pl, 12.5mg/100|il and 6.25mg/l OOpI using sterile distilled water. Similar concentrations were done with the antifungal drug triazole as the positive control. Assessment of the efficacy of different concentrations of the Aloe species leaf extracts against Fusarium oxysporum and Pythium ultimum was carried out using the agar disc diffusion method. Paper discs impregnated with different concentrations of the Aloe extracts were placed in the petri plates and zones of inhibition measured in millimeters for 11 days. SRAP primers produced 893 genetic loci with percentage polymorphic loci of 56.8%. Nei genetic distance for the populations ranged from 0.094 to 0.362 with 9% and 91% variation among
xiii
populations and within individuals, respectively. Organic crude extracts of A. Sccundijlora showed the highest activity (Mean inhibition = 16.01 mm) against the test fungi compared to A. later ilia (Mean inhibition = 13.09 mm) and A. turkanensis (Mean inhibition = 11.04 mm). The crude extracts showed higher activity against F. oxysporum than P. ultimum; but there was no activity for all the crude extracts at 6.25mg/ml. None of the crude extracts showed higher activity than the commercially used fungicide triazole. The findings of this study could form basis for better conservation of the genus which has potential to control fungi of agricultural importance alongside other control measures.
Keywords: Aloe species, Sequence Related Amplified Polymorphism (SRAP), Fusarium
oxysporum, Pythium ultimum.

Micheni, C. M. (2015). Genetic Diversity Of Aloe Species In Kenya And The Efficacy Of Aloe Secundiflora, Aloe Lateritia And Aloe Turkanesis On Fusarium Oxysporum And Pythium Ultimum
. (Thesis). University of Nairobi. Retrieved from http://hdl.handle.net/11295/95984

Note: this citation may be lacking information needed for this citation format:Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16th Edition):

Micheni, C M. “Genetic Diversity Of Aloe Species In Kenya And The Efficacy Of Aloe Secundiflora, Aloe Lateritia And Aloe Turkanesis On Fusarium Oxysporum And Pythium Ultimum
.” 2015. Thesis, University of Nairobi. Accessed January 21, 2019.
http://hdl.handle.net/11295/95984.

Note: this citation may be lacking information needed for this citation format:Not specified: Masters Thesis or Doctoral Dissertation

Micheni CM. Genetic Diversity Of Aloe Species In Kenya And The Efficacy Of Aloe Secundiflora, Aloe Lateritia And Aloe Turkanesis On Fusarium Oxysporum And Pythium Ultimum
. [Internet] [Thesis]. University of Nairobi; 2015. [cited 2019 Jan 21].
Available from: http://hdl.handle.net/11295/95984.

Note: this citation may be lacking information needed for this citation format:Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Micheni CM. Genetic Diversity Of Aloe Species In Kenya And The Efficacy Of Aloe Secundiflora, Aloe Lateritia And Aloe Turkanesis On Fusarium Oxysporum And Pythium Ultimum
. [Thesis]. University of Nairobi; 2015. Available from: http://hdl.handle.net/11295/95984

Note: this citation may be lacking information needed for this citation format:Not specified: Masters Thesis or Doctoral Dissertation

► Recent investigations of coral reef biology have focused on the global biogeography and host specificity of Symbiodinium, a diverse group of dinoflagellates that symbiotically associate…
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▼ Recent investigations of coral reef biology have focused on the global biogeography and host specificity of Symbiodinium, a diverse group of dinoflagellates that symbiotically associate with many marine organisms, including reef-building corals. Despite this, few studies have investigated the genetic structure of Symbiodinium at the population level. One suitable system to investigate Symbiodinium population genetics of a single host across a global range is the facultatively symbiotic anemone Aiptasia. In order to determined the specificity and population genetic structure of Symbiodinium communities associated with Aiptasia spp., 356 anemones were sampled from 18 locations throughout the world. Symbiodinium diversity was assessed using a variety of
v
molecular markers that measure diversity from the level of sub-generic clades to populations, including restriction fragment length polymorphisms (RFLPs) of 18S-rDNA, denaturing gradient gel electrophoresis (DGGE) of the internal transcribed spacer 2 (ITS2) rDNA, flanking region sequences of two microsatellite loci, and allelic variation at six microsatellite loci specific for Symbiodinium Clade B. These data revealed that, with the exception of individuals from the Florida Keys, a single phylotype of Symbiodinium clade B (ITS2 “type” B1) associates with Aiptasia throughout the world. Furthermore, strong population structure was detected across local, regional, and global geographic scales, suggesting limited gene flow among most Symbiodinium populations. The high genetic structure of Symbiodinium populations and the association with one particular symbiont lineage across large geographic scales suggests strong regional endemism and the existence of specificity in Aiptasia-Symbiodinium symbioses. This work represents a contribution towards our understanding of the ecology and evolution of cnidarian-Symbiodinium endosymbioses.
Advisors/Committee Members: Santos, Scott (advisor).

► Understanding how captivity affects the behavioral and development traits of a species is important for management and conservation in zoos. The ecology of squirrel monkeys…
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▼ Understanding how captivity affects the behavioral and development traits of a species is important for management and conservation in zoos. The ecology of squirrel monkeys (Saimiri sp.) may be different in captivity than in their natural environment. I investigated five common ecological aspects: reproduction, vigilant behaviors, life history traits, and generational changes in seasonality. Reproduction in squirrel monkeys is naturally seasonal with speculation as to the environmental factor with the greatest influence. In captivity, different types of habitats used to house squirrel monkeys may affect seasonality of reproduction. Those individuals housed in outdoor enclosures maintained a seasonal peak of births while those monkeys kept in indoor enclosures reproduced throughout the year. These habitat-based differences in reproduction allowed for analysis of environmental variables, and temperature had a large impact on births.
Captivity also provides the opportunity to determine whether differences exist in vigilant responses of individuals to playbacks of alarm calls, in regards to whether anti-predator responses are innately predisposed or require experience. Captive squirrel monkeys presented with alarm, predator, and control sounds elicited a greater amount of vigilant behaviors to alarm calls compared to other sounds. However these behaviors were not maintained for a minute after the playback. Interestingly, a “group personality” seemed to be exhibited; responses were not related to group size or type of enclosure. Captive squirrel monkeys were naïve yet still able to correctly respond to alarm calls by displaying vigilant behaviors.
Differences due to captive environments may affect life history traits of squirrel monkey populations. Variation in life history traits occurs between sexes, zoos, and generations of squirrel monkeys maintained in captivity. Prospective analyses predict that juvenile and adult survivals have the greatest impacts on population growth. Fertility, however, is the demographic trait that contributes the most to changes in population size based on a retrospective analysis. The seasonality of reproduction has previously been shown to vary depending on type of habitat. With several generations of squirrel monkeys established in captivity, change in reproduction timing allowed for testing of whether this change is due to plasticity or selection. Using pedigree data, differences between when mothers and daughters have their offspring reflects environmental influences, rather than heritability. Seasonal reproduction is significantly different between the wild and captive generations, however not between the two captive generations.
Advisors/Committee Members: Dobson, F. Stephen (advisor).

► Ariids or sea catfishes are one of the two otophysan fish families (out of 67 families in four orders) that inhabit primarily marine and brackish…
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▼ Ariids or sea catfishes are one of the two otophysan fish families (out of 67 families in four orders) that inhabit primarily marine and brackish waters, although some ariid species occur strictly in fresh waters. The Ariidae includes over a 150 species and many are of primary importance for tropical fisheries. Their classification has remained in disarray and recent studies that have intended to elucidate relationships among ariids have mostly focused on taxa from restricted geographic areas and comprehensive phylogenies are lacking. Furthermore, few efforts have been made to hypothesize biogeographic scenarios and evolutionary trends among ariids. This study inferred molecular phylogenies (up to ~4 kb) for ariids based on the most inclusive taxon sampling to date (123 species/entities). The results support the monophyly of the Ariidae (four anatomical and three molecular synapomorphies) and the sister-taxa relationship between ariids and the Malagasy family Anchariidae. The Ariidae is divided into two
basal lineages. The Galeichthyinae, new subfamily, includes one genus and four species from southern Africa (three species) and southwestern South America (one species), representing a remarkable case of transoceanic disjunction. Molecular data provided fully-resolved and well-supported phylogenies for galeichthyines, indicating that the South American species is nested within the African clade. An earlier study attributed galeichthyines’ disjunct distribution to vicariance promoted by the final separation of Africa and South America (~105 mya). However, chronological estimations via molecular clocks show that the timing of intercontinental divergence was 15.4–2.5 mya, implying transoceanic dispersal or recent vicariance. The subfamily Ariinae includes the remaining taxa (~97% of ariid diversity). The topologies support the monophyly of ariines but up to ten genera previously validated are incongruent with the molecular phylogenies. New World ariines were paraphyletic and Old World ariines were grouped into a well-supported clade further divided into subclades mostly restricted to major Gondwanan landmasses. The general area cladogram derived from the area cladograms of ariines and other fish groups is largely congruent with the geological area cladogram of Gondwana. Nonetheless, molecular clock analyses provided highly variable estimations on the timing of ariine diversification (~28–105 mya). Habitat distributions (freshwater vs. marine) were optimized onto the phylogeny to test whether freshwater ariids are primitive (i.e., retain the ancestral freshwater otophysan condition) or derived (i.e., involve marine-to-freshwater transitions). The reconstructions support the latter scenario, suggesting a single invasion of marine waters at the root of the ariid tree followed by multiple events of freshwater recolonization in the Ariinae. Ariids provide an extraordinary example of bidirectional habitat transitions in fishes.
Advisors/Committee Members: Armbruster, Jonathan (advisor).

► The function and evolution of avian plumage coloration has been the subject of many studies over the past decade, but virtually all of this research…
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▼ The function and evolution of avian plumage coloration has been the subject of many studies over the past decade, but virtually all of this research has focused on the plumages of sexually mature individuals. The color and pattern of juvenal plumage, which is worn only for the first few months of life by altricial songbirds, remains essentially unstudied. To examine how juvenal plumage functions in intraspecific contexts, we developed a three-pronged approach designed to uncover the evolutionary origins and current adaptive functions of several juvenal plumage traits.
First, we developed the idea that distinctive juvenile appearance may be a signal of sexual immaturity, serving to reduce aggression from conspecific adults. We used a comparative approach to test this hypothesis in the thrushes (Family Turdidae) and found that distinctive juvenile appearance was significantly correlated with increased risk of conspecific aggression. The observed associations are consistent with our hypothesis that the benefits of signaling sexual immaturity have driven the evolution of distinctive juvenal plumage. Second, we tested the applicability of the comparative study results by employing a field study of eastern bluebirds, Sialia sialis. We tested the hypothesis that spotty plumage of eastern bluebird juveniles’ signals age, thereby decreasing aggression from territorial adults, by measuring the aggressive responses of adult bluebird males to different combinations of simultaneously presented taxidermic mounts. We found that territorial males do not recognize juvenile-specific plumage, but avoid attacking intruders that lack adult plumage characters. Third, we tested the idea that plumage color may serve as a signal of quality in fledgling eastern bluebirds and that parental feeding decisions are influenced by differences between offspring with respect to plumage color. Fledglings were presented in pairs and parental investment was scored as a percentage of feeding attempts to each individual. Our results support the hypothesis that feather coloration of male bluebird fledglings affects the care they receive from parents. Eastern bluebird parents appear to use juvenal plumage coloration as a signal to assess the relative quality of offspring after fledging and to adjust parental investment in a manner that maximizes their reproductive success.
Advisors/Committee Members: Hill, Geoffrey (advisor).

► Tropical South America is renowned for its unparalleled biodiversity. Among vertebrates, fish diversity exceeds that of any other group. Estimates of total Neotropical fish richness…
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▼ Tropical South America is renowned for its unparalleled biodiversity. Among vertebrates, fish diversity exceeds that of any other group. Estimates of total Neotropical fish richness range between 5000 and 8000 species, of which approximately 3600 (45–72%) are currently described; and of described species, nearly 20% (>700 spp.) are catfishes in the Neotropical-endemic family Loricariidae. Loricariid catfishes, popularly known as plecos in the aquarium trade, are distinguished by their armor plating, ventral oral disk, and highly derived jaw structure and function. Loricariids have likely existed in South American rivers in close to their modern form since at least the Late Cretaceous, and they are part of a superfamilial lineage (Loricarioidea) that is sister to all other catfishes, and has likely inhabited South American rivers since well into the Early Cretaceous. Today, loricariids have radiated to consume a variety of basal food resources including algae, detritus, seeds, sponges, insects, and even wood, the surface layers of which are gouged into by specialized taxa having hypertrophied jaw muscles and teeth shaped like adzes.
In this dissertation, I attempt to fill major gaps in the knowledge of loricariid taxonomy, jaw morphological and functional diversity, trophic ecological structure, and historical biogeography. My taxonomic research has resulted in the discovery and/or description of dozens of new loricariid species and at least three new genera. Published results of this work are summarized in Appendix I. In chapter two of this dissertation, I describe jaw morpho-functional diversity across a diverse assemblage of 25 species, 12 genera, five tribes, and two subfamilies of loricariids from the upper Amazon Basin in Northern Peru. In chapter three, I describe gross aspects of loricariid assemblage trophic structure as revealed by carbon and nitrogen isotope data from 19 loricariid assemblages ranging in species richness from two to 16 species, and geographically broadly distributed across northern South America. In chapter 4, I review the geological and hydrological history of the Guiana Shield, a highly biodiverse and geologically ancient region of northern South America which shelters a broad range of basal and derived loricariid lineages. From these studies, it is clear that tremendous loricariid diversity accumulated in the Neotropics gradually over tens of millions of years and across a broad geographic range, and that their novel oral morphology has likely been key to their diversification across a variety of basal resources consumed almost exclusively by invertebrate faunas at more temperate latitudes.
Advisors/Committee Members: Armbruster, Jonathan (advisor).

► Conversion of land from an undeveloped state into agricultural or urban areas is widespread. Urban areas in particular are growing both in size and number…
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▼ Conversion of land from an undeveloped state into agricultural or urban areas is widespread. Urban areas in particular are growing both in size and number globally. Such land use changes can potentially have negative consequences for organisms such as amphibians, many of which require aquatic and terrestrial environments to complete their life cycle. I conducted herpetofaunal richness surveys of several watersheds in western Georgia, USA, subject to varying degrees of urbanization or pasture land uses, which revealed amphibians are particularly sensitive to urban areas, but not pasture lands. Reptiles showed the opposite response (i.e., more reptile species were found in urban areas). The results of this survey prompted a more detailed study of the stream-breeding salamander, Eurycea cirrigera (two-lined salamander). I found that this species has a reproductive output in urban streams equal to conspecifics in reference environments, but that survivorship of larvae to metamorphosis was much lower in urban streams. Path
analysis of potential environmental factors contributing to this putative decline in survivorship revealed frequent and intense flooding in urban environments is the most probable cause for observed declines. To validate this finding, I created a series of experimental streams (flumes), in which water flow and substrate were manipulated. I found salamanders were more likely to be eroded from experimental flumes at lower water velocities when flumes contained sandy substrates without rocky cover, a streambed condition common in urban streams. Taken together, field and experimental data strongly suggest an altered hydrology in urban areas is one of the leading factors causing stream-breeding salamander decline in urban habitats. In addition, I followed my studies on hydrological effects by evaluating growth of the two-lined salamander across an urban – forest gradient. I found that larvae in urban streams grew faster than larvae in forested streams. The benefit of faster larval growth could explain the persistence of the two-lined salamander in urbanized watersheds. Finally, I described shifts in consumed prey by two-lined salamanders that accompany urbanization. While these shifts were not dramatic, the descriptions I offer provide a foundation for describing food web dynamics in urban habitats. In total, urbanization dramatically alters herpetofaunal assemblages in and around streams. Those species that are not extirpated apparently suffer survivorship costs and shifts in growth and diet. Information from assemblage-wide and species-specific perspectives, provided here, is needed to increase our ability to ameliorate effects of urbanization on stream-dwelling amphibian species.
Advisors/Committee Members: Guyer, Craig (advisor).

► The trade in live vertebrates is a threat to biodiversity, homogenizing distinct flora and fauna, introducing invasive species and parasites, and depleting wild populations. Because…
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▼ The trade in live vertebrates is a threat to biodiversity, homogenizing distinct flora and fauna, introducing invasive species and parasites, and depleting wild populations. Because records of live vertebrates imported or exported by the United States are maintained by the US Fish and Wildlife Service (USFWS), a complete record of species in trade can be generated for this country. I obtained USFWS records for 6 taxonomic groups (amphibians, turtles, lizards, snakes, birds, and mammals) from 1968 – 2006 and used these trade data to quantify patterns in trade over time, and assess its importance as an invasion pathway and contribution to biological homogenization. The United States transported over 4200 species of terrestrial vertebrates during 1968 – 2006. Because trade in live vertebrates is dynamic, there have been changes in the species used for trade, quantities of individuals traded, and trading countries. I found that trade in live
vertebrates contributes to both mechanisms of biological homogenization, extinctions and introductions. Based on Monte Carlo sampling, the number of species traded, established, and threatened with extinction were not randomly distributed among vertebrate families. Vertebrate families that were traded preferentially were also more likely to be established or threatened with extinction, compared to families that were not traded preferentially. I followed this research with additional work that focused solely on introductions. I used USFWS trade data to estimate the number of species that have transitioned successfully through the five stages of the invasion process, and compared those transition rates to those expected by the “tens rule”. I found that roughly 10% of all vertebrate species imported to the United States were introduced. Birds and snakes did not differ from what was expected by the “tens rule” for the establishment transition. Amphibians, lizards and snakes exhibited a high transition success at the establishment stage (~ 45%). All vertebrate species differed from the “tens rule” in the final spread stage, their transition success was approximately 40%. Finally, I used human influence variables (import pressure, previous invasion success elsewhere, monetary value, wild caught vs. captive bred) to assess their ability to predict introduction and establishment success among vertebrate species imported to the United States. Import pressure was measured as the average number of individuals imported and separated by time period into past and recent import pressure. Among the a priori models, those that included past import pressure were the best models consistently across all 6 vertebrate groups. For specific taxonomic groups, previous success elsewhere was the most important variable among the top models, and improved the prediction of introduction and establishment success.
Advisors/Committee Members: Guyer, Craig (advisor).

Romagosa, C. (2009). United States Commerce in Live Vertebrates: Patterns and Contribution to Biological Invasions and Homogenization
. (Doctoral Dissertation). Auburn University. Retrieved from http://hdl.handle.net/10415/1711

Romagosa C. United States Commerce in Live Vertebrates: Patterns and Contribution to Biological Invasions and Homogenization
. [Doctoral Dissertation]. Auburn University; 2009. Available from: http://hdl.handle.net/10415/1711

Auburn University

21.
Hunter, Rebecca.
Phylogeography and population structure of Antarctic ophiuroids: effects of life history, oceanography and paleoclimatology
.

► The Antarctic landmass and surrounding continental shelf have been isolated for over 24 million years. Geographic and thermal isolation have resulted in a highly endemic,…
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▼ The Antarctic landmass and surrounding continental shelf have been isolated for over 24 million years. Geographic and thermal isolation have resulted in a highly endemic, diverse benthic marine fauna. This fauna has been relatively well characterized morphologically, but little is known about the evolutionary history, genetic diversity and population genetic structure of Antarctic benthic marine invertebrates. Several important questions remain largely unanswered, including 1) are circumpolar species genetically homogeneous throughout their range, 2) are non-endemic species maintaining
connectivity between populations distributed in Antarctica and South America, and 3) how does early life history influence dispersal throughout Antarctica?
This research examined phylogeographic patterns within four Antarctic brittle stars (ophiuroids). Ophiuroid species were chosen that differed in their mode of development (i.e., presence/absence of a pelagic larval stage) and geographic distribution. A non-endemic brooding species, Astrotoma agassizii, was evaluated in order to assess connectivity across a major oceanographic barrier separating Antarctic and South American populations. Three Antarctic endemics, Ophiurolepis gelida, O. brevirima and Ophionotus victoriae, all possessing some form of pelagic larvae, were obtained from various locations around Antarctica in order to characterize their population structure and levels of gene flow throughout the Antarctic continental shelf.
Analysis of intraspecific mitochondrial sequence data revealed several interesting patterns. First, all species showed evidence of restricted connectivity between major geographic regions in the Antarctic, subantarctic and/or South America (depending on sampling), regardless of developmental mode. Additionally, cryptic divergence and/or speciation were recovered in all cases. Second, the brooding species, A. agassizii, displayed evidence of greater connectivity within geographic regions compared to species with pelagic larvae. These results suggest that phylogeographic patterns are not easily predicted for Antarctic brittle stars, and ophiuroid diversity is underestimated in the Southern Ocean. These generalizations likely apply to other Antarctic marine invertebrates, and suggest that much more research will be required to quantify Southern Ocean biodiversity and fully understand the contemporary and historical processes driving evolution in this region.
Advisors/Committee Members: Halanych, Kenneth (advisor).

► Oxidative stress is regarded as the damage to a biological system caused by reactive oxygen species (ROS) when the prooxidant overwhelms the antioxidant defense and…
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▼ Oxidative stress is regarded as the damage to a biological system caused by reactive oxygen species (ROS) when the prooxidant overwhelms the antioxidant defense and repair ability. Growing evidence reveals that oxidative stress is a major contributor to aging and neurodegeneration. P62 is a scaffold protein that is utilized for cell signaling, receptor trafficking, and inclusion formation. P62 knockout mice exhibit Alzheimer’s Disease-like phenotype. The structure and function of p62, ROS formation and oxidative damage to macromolecules, the antioxidant defense system, the relationship among p62, oxidative stress, aging, and neurodegenerative disease were reviewed in Chapter I.
Declined p62 expression levels were observed in Alzheimer’s Disease (AD) brains compared to tissue from normal individuals. My hypothesis was that reduced p62 level might be caused by oxidative damage to the p62 promoter. In order to test this hypothesis, two specific objectives were undertaken: (1) examine age-associated oxidative damage to the p62 promoter in AD; (2) examine whether this damage is common in various neurodegenerative disease. In Chapter II, we showed that oxidative damage to the p62 promoter was significantly higher in DNA from AD brain than normal brain. Also, this damage was age-dependent in both WT mice and normal brains. The negative correlation between oxidative damage to the p62 promoter and the p62 expression level was demonstrated in human brains, mice, and HEK cells. In Chapter III, we showed that no genetic variance was found between the p62 promoter in normal and diseased brains. However, oxidative damage to the p62 promoter was significantly higher in various neurodegenerative diseases than normal brains. Decreased activity and induction of the p62 promoter were caused by oxidative damage to the p62 promoter and the deletion of Sp-1 binding site. Altogether, these findings revealed that p62 level was regulated by oxidative damage to the p62 promoter.
P62 regulation and future works were summarized in Chapter IV. Proteasome or autophagy inhibition up-regulates p62 protein levels. Decreased p62 level results in the reduced delivery of substrate to autophagy, leading to more damaged organelles. Since p62 knockout mice showed higher oxidative stress, the mechanism leading to this result will be further investigated and mitochondria dysfunction will be examined in WT, p62 knockout, and p62 over-expressed mice.
Advisors/Committee Members: Wooten, Marie (advisor).

► Viruses are the most abundant yet uncharacterized biological entities on the planet. This thesis is a survey of viral communities in soil, activated sludge (AS),…
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▼ Viruses are the most abundant yet uncharacterized biological entities on the planet. This thesis is a survey of viral communities in soil, activated sludge (AS), and influent (IN). Both culture-dependent and culture-independent techniques were used to assess the viral communities. Linker-amplified shotgun subclone viral metagenomic libraries were constructed from all environments and a bacteriophage culture collection was constructed from the activated sludge sample for use in comparison of the two culture assessment methods.
The bioinformatics analysis of the metagenomic libraries revealed that the viral communities studied were not well characterized in the GenBank databases and supported the hypothesis that different environments harbor distinct populations of viruses.
Advisors/Committee Members: Liles, Mark (advisor).

▼ Polyketides are structurally diverse bacterial secondary metabolites, many of which have antibiotic or anti-cancer activity. Modular polyketide synthase (PKS) enzymatic complexes contain conserved ketoacyl synthase (KS) domains, and most PKS biosynthetic pathways exceed 30 kb in size. A fosmid metagenomic library constructed from soil at the Hancock Agricultural Research Station in Hancock, WI, (18,432 clones, average insert of 42 kb) was spotted onto a nylon membrane. The macroarray was screened using a degenerate DNA probe targeting the KS domain. Thirty-four clones containing KS domains were identified by Southern hybridization; however, only 21 of the 34 PKS-positive clones produced a PCR product. Interestingly, most of the clones (8 out of 13) that were PCR-negative were nontheless KS-positive by Southern blot hybridization. DNA sequences from a KS-containing clone that was consistently PCR-negative have revealed a biosynthetic pathway that is divergent from known pathways,
and is hypothesized to have an origin from the newly described bacterial division Acidobacteria that is prevalent within soils yet has few cultured representatives.
Advisors/Committee Members: Liles, Mark (advisor).

► I examined microhabitat characteristics affecting the occupancy of wintering birds in a southeastern bottomland forest with repeated point counts at 186 sites. Models were derived…
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▼ I examined microhabitat characteristics affecting the occupancy of wintering birds in a southeastern bottomland forest with repeated point counts at 186 sites. Models were derived a priori based on published literature and personal observations. I assessed 34 species and their microhabitat preferences within the Choctawhatchee River Basin. I then created microhabitat groups based on all habitat associations that allowed for a simplified interpretation of results. Microhabitat characteristics were important for 25 of 34 species of birds and were important predictors their occupancies 34 times. The occupancy of species was influenced similarly by physiognomic and floristic characteristics; the former influenced occupancy of 12 species and the latter occupancy of 19 species. The basal area of tupelo (Nyssa) was the most important floristic predictor, and for five of six species it negatively affected the presence of birds. Number of woody stems (< 10 cm dbh) was the most important physiognomic predictor of species occupancy. Woody stems affected occupancies of four species. Presence of standing water and oak-hickory (Quercus + Carya aquatica) community affected occupancies of three species. Oak-gum-cypress (Quercus + Nyssa + Taxodium distichum) community affected occupancies of two species. The probability of detecting birds was most frequently affected by date and observer differences. Also affecting the probability of detection were wind, temperature, and time after sunrise. Microhabitat is an important component of habitat selection by birds and should be incorporated into models of occupancy that are used for conservation purposes. My study provides empirically tested associations between occupancy and microhabitat characteristics, and can provide a starting point for future habitat modeling efforts.
Advisors/Committee Members: Geoffrey, Hill (advisor).

▼ The gram-negative bacterium Pseudomonas aeruginosa catalyzes the conversion of ricinoleic acid into a novel trihydroxy fatty acid, 7, 10, 12-trihydroxy-8(E)-octadecenoic acid (TOD), that has a potent antifungal activity against important crop pathogens, including Magnaporthe grisea the causative agent of rice blast disease. Natural crop-protecting agents such as TOD offer several advantages over synthetic agents, including improved ecological compatibility and environmental safety. Unfortunately, because many naturally occurring crop-protecting agents are produced only in trace amounts, it has been difficult to isolate large enough quantities of these antimicrobial agents to be economically feasible. Thus, a bacterium such as P. aeruginosa that is genetically amenable and produces an antifungal agent is ideal for genetic manipulation to achieve improved TOD production. The long-term goal of this research is to develop efficient processes for improving production of TOD from P. aeruginosa to mass-produce an economically competitive and environmentally friendly biological crop protection agent. As an initial step towards this goal, a genetic study was undertaken to identify the genes that are required for production of TOD in P. aeruginosa. In order to facilitate the genetic screen, a bioassay was developed to assess TOD’s antifungal activity against M. grisea in 96-well microtiter plates using either pure TOD or P. aeruginosa culture supernatants. In order to identify the genes involved in the bioconversion, a transposon mutagenesis was performed and a library of ~15,000 Tn5-B21 insertion mutants of the P. aeruginosa strain NRRL B-23260 (an environmental isolate) was constructed. From the genetic screen, 28 transposon insertion mutants that were defective for TOD production were identified. Molecular studies identified eleven mutants that appeared to have single transposon insertions. Genetic mapping of these eleven mutants was conducted to identify the genes that had been interrupted by transposon insertion. From this analysis, eight genes were identified including genes encoding alkylated DNA repair proteins, ferrous iron transport proteins, pseudouridylate synthase, a hypothetical protein/magnesium transport protein, a transport protein of ABC transport, and XcpP of the general secretory pathway. Three of the mutants have been successfully complemented with the wild-type genes to demonstrate their involvement in the microbial conversion of ricinoleic acid to TOD.
Advisors/Committee Members: Suh, Sang-Jin (advisor).

► The family Chiasmodontidae, commonly known as swallowers, comprises four genera and 33 species distributed in the meso and bathypelagic regions of the Atlantic, Pacific, Indian…
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▼ The family Chiasmodontidae, commonly known as swallowers, comprises four genera and 33 species distributed in the meso and bathypelagic regions of the Atlantic, Pacific, Indian and Southern Oceans. The species of Chiasmodon and Pseudoscopelus have disjunct distribution, and those of Dysalotus and Kali, wide distributions.
The genus Chiasmodon is composed of seven species, two of them new: C. niger; C. subniger; C. braueri; C. microcephalus; C. pluriradiatus; C. asper n. sp.; and C. harteli n. sp. Pseudoscopelus has 16 species, five of them new: P. scriptus; P. sagamianus; P. altipinnis; P. cephalus; P. obtusifrons; P. scutatus; P. aphos; P. parini; P. astronesthidens; P. australis; P. pierbartus; P. bothrorrhinos n. sp.; P. lavenbergi n. sp.; P. paxtoni n. sp.; P. cordilluminatus, n. sp.; and P. odontoglossum sp. n. Dysalotus has only three species, one new: D. alcocki; D. oligoscolus; and D. acanthobrychos. Kali has seven species, two of them new: K. indica; K. kerberti; K. macrodon; K. macrura; K. parri; K. colubrina, n. sp.; and K. falx, n. sp.
The chiasmodontids have several morphologic adaptations related to life in the deep-sea and swallowing of enlarged preys. Those characteristics include the reduction of some bones and muscles, diverse dentition, enlarged mouth, a very distensible stomach and body walls, photophores, and the presence of superficial neuromasts on head and body. One of the most remarkable characteristics is the innumerous superficial neuromasts, which are present in all chiasmodontids. The superficial neuromasts are more concentrated in the head, but are also present on body along the trunk lateral-line canal, on upper and lower lobes of the caudal fin, and dorsal part, anterior and to the first-dorsal fin. The distribution of neuromasts is described, as well as their innervation.
A phylogenetic analysis was made based on 161 morphological characters obtained from osteology, myology, lateral line system, dentition and miscellaneous. The monophyly of the Chiasmodontidae is corroborated by 24 synapomorphies. Within the chiasmodontids, two major clades are formed: the Chiasmodon clade is composed of Chiasmodon and Pseudoscopelus, and supported by 18 synapomorphies; and the Kali clade is composed by Dysalotus and Kali, and supported by 22 synapomorphies. The monophyly of the genus Chiasmodon is supported by 16 synapomorphies; Pseudoscopelus, by 12 synapomorphies; Dysalotus, by 18 synapomorphies; and Kali, by 23 synapomorphies.
Advisors/Committee Members: Armbruster, Jonathan (advisor).

► The growing interest in the reproductive benefits of biasing offspring sex ratios in avian species has generated curiosity and provided much insight into the potential…
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▼ The growing interest in the reproductive benefits of biasing offspring sex ratios in avian species has generated curiosity and provided much insight into the potential factors and mechanisms controlling sex-ratio adjustment. Differing offspring sex ratios often occur in response to changes in the environment. Of particular interest, but less understood, are the mechanisms regulating primary (pre-ovulatory) sex-ratio adjustment. Recently, a number of bird studies have suggested that females (the heterogametic sex) are capable of using primary mechanisms to adjust offspring sex ratios; however the mechanism responsible for this is unknown.
Sex of offspring is determined in the first meiotic division when one sex chromosome is retained in the oocyte while the other segregates to the polar body. During this time, follicular steroid production is limited primarily to progesterone (P4) and so it has been suggested that maternal steroids, which are sensitive to environmental perturbations, could also influence sex chromosome segregation. Additionally, primary offspring sex ratios have been shown to be affected by some of the same environmental factors that are known for inducing changes in an individual’s hormonal milieu. Researchers studying the effects of elevated levels of maternal steroids on primary sex ratio have mainly done so by administering pharmacological doses of exogenous hormones to mothers, but none have examined endogenous hormones at meiosis I (critical time in sex determination).
We manipulated both diet quality and perceived availability in breeding female zebra finches (Taeniopygia guttata) so that we could examine the effect this changing factor would have on natural levels of P4, corticosterone (CORT), and testosterone (T) in circulation during meiosis I and throughout the day. We found that females fed the high quality diet produced significantly more male offspring (81%) and exhibited moderately low to very low levels of these steroids. Females fed the low quality diet produced 38% males and had the highest P4 levels, but relatively low levels of CORT. When the high quality diet was perceived to be restricted females produced 46% males and had the highest CORT levels, while P4 remained relatively low. All three steroids reached their peak during the period of meiosis I; however T levels were very low (below 1ng/ml) in all diet treatments throughout the day. Our results suggest that no one hormone is responsible for primary sex ratio adjustment in this species. It appears that natural levels of maternal steroids, particularly P4 and CORT, in circulation during meiosis I play an integral yet complex role in the mechanism.
Advisors/Committee Members: Mendonca, Mary (advisor).

► Larvae of diptera of the family Sarcophagidae from bogs in Mississippi, Alabama, and Florida were collected, reared, and identified to species. Additionally, the effect of…
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▼ Larvae of diptera of the family Sarcophagidae from bogs in Mississippi, Alabama, and Florida were collected, reared, and identified to species. Additionally, the effect of sarcophagid larvae on nutrient uptake in white-topped pitcher plant leaves (Sarracenia leucophylla) was examined at Crawford bog in south Alabama. The influence of sarcophagid larvae on nutrition of pitcher plants has not been previously recorded in the literature.
I reared Sarcophaga sarraceniae, Fletcherimyia abdita , and F. celarata from pitchers of S. leucophylla. In Alabama, all three species occurred at Crawford Bog while only S. sarraceniae and F. abdita occurred at Splinter Hill Bog. I reared F. abdita from pitchers of S. alata occurring in Desoto West Bog in Mississippi. Two species of sarcophagids, F. rileyi and F. jonesi, were reared from pitchers of S. flava. Both occurred at Sumatra Bog in Florida, while only F. rileyi was found at Crawford Bog. I also calculated sarcophagid larval frequencies in S. leucophylla and S. flava at Crawford Bog during 2004 and 2005. In 2004, 70% of S. leucophylla leaves surveyed contained at least one sarcophagid larva. In 2005, only 58% of leaves contained larvae, but among these, four were occupied by multiple larvae. Eighty-six percent and 94% of S. flava leaves in 2004 and 2005 respectively were occupied by at least one larva. During both years, 4 of the occupied pitchers contained multiple larvae.
Nutrition field experiments were conducted at Crawford Bog during the summers of 2004 and 2005. I demonstrated a strong positive relationship between the addition of prey and leaf concentrations of macronutrients (N, P, and K). In each experimental group, pitchers supplemented with prey and with prey plus larvae contained significantly higher nutrient levels than the other experimental conditions (except 2004 potassium control). Additionally, I demonstrated that larvae do not negatively affect plant nutrition. Pitchers supplemented with prey plus sarcophagid larvae showed a strong trend towards higher nutrient levels than pitchers with prey only.
Advisors/Committee Members: Folkerts, Debbie (advisor).

► The number of prokaryotes known to participate in intercellular signaling is growing. The objective of this research was to determine if Legionella species are able…
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▼ The number of prokaryotes known to participate in intercellular signaling is growing. The objective of this research was to determine if Legionella species are able to communicate through the use of intercellular signals with other bacteria and with eukaryotic hosts. The evaluation of intercellular signaling in L. pneumophila was conducted in three phases: i) determine if Legionella species produce intercellular signals; ii) determine if L. pneumophila responds to signals produced by unrelated microorganisms, and iii) evaluate if L. pneumophila can respond to signals or other metabolites produced by its natural, protozoan hosts.
Among bacteria, known intercellular signals include N-acyl homoserine lactones (AHSL), autoinducer-2 (AI-2), and quinolone autoinducers. In the evaluation of Legionella species’ ability to produce signaling metabolites, biological sensors that detect
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AHSL, AI-2, and quinolone autoinducers were used. The data from each of the trials demonstrated conclusively that Legionella species do not produce AHSL, AI-2, or quinolone signals.
In the evaluation of the ability of L. pneumophila to respond to interspecies or inter-kingdom signals, the pathogen was exposed to supernatants of signal producing microorganisms and that of protozoa known to support their intracellular growth. An evaluation of the protein profile of L. pneumophila following its exposure to these supernatants by two-dimensional electrophoresis (2-DE) revealed the expression of multiple proteins. Subsequent analysis by matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) aided in the presumptive identification of many of these proteins.
Of the 40 proteins that were identified, 36 were differentially expressed in L. pneumophila following exposure to the supernatants of signal producing bacteria. These proteins included global stress protein GspA and a 24kDa macrophage induced protein. Following exposure to protozoa, 36 proteins were identified as a part of the L. pneumophila response and include a Legionella long chain fatty acid transporter and cold shock domain protein CspA. In terms of its protein expression, the reaction demonstrated by L. pneumophila in the presence of unrelated prokaryotes and potential host protozoa represented a stress response and suggested that L. pneumophila can respond to these organisms via intercellular signaling.
Advisors/Committee Members: Barbaree, James (advisor).